Variant report

Variant	rs13321995
Chromosome Location	chr3:194818087-194818088
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:194818030-194818233	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:194817916-194818294	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr3:194817999-194818251	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr3:194817941-194818350	MCF10A-Er-Src	breast:	n/a	chr3:194818174-194818183 chr3:194818122-194818137 chr3:194818174-194818183 chr3:194818175-194818182
5	STAT3	chr3:194817954-194818268	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr3:194818005-194818271	MCF10A-Er-Src	breast:	n/a	n/a
7	MAX	chr3:194817969-194818351	K562	blood:	n/a	chr3:194818174-194818183 chr3:194818122-194818137 chr3:194818174-194818183 chr3:194818175-194818182
8	USF1	chr3:194817989-194818265	K562	blood:	n/a	n/a
9	MYC	chr3:194817899-194818350	MCF10A-Er-Src	breast:	n/a	chr3:194818174-194818183 chr3:194818122-194818137 chr3:194818174-194818183 chr3:194818175-194818182
10	FOS	chr3:194817958-194818310	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr3:194818015-194818238	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:194817020..194819382-chr3:194820062..194821788,3	K562	blood:
2	chr3:194817667..194819291-chr3:194820083..194822467,2	MCF-7	breast:

Variant related genes	Relation type
XXYLT1	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs9853846	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9859044	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13321995	ATP13A5	cis	cerebellum	SCAN
rs13321995	DLG1	cis	cerebellum	SCAN
rs13321995	C3orf59	cis	cerebellum	SCAN
rs13321995	LOC348840	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194791000-194821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:194802000-194826800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:194804000-194818200	Weak transcription	Right Ventricle	heart
4	chr3:194806800-194826400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:194808400-194823000	Weak transcription	Adipose Nuclei	Adipose
6	chr3:194808600-194823000	Weak transcription	K562	blood
7	chr3:194808600-194827000	Weak transcription	Fetal Brain Female	brain
8	chr3:194808800-194821400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:194808800-194824800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:194814400-194823000	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:194814600-194827800	Enhancers	Fetal Heart	heart
12	chr3:194815000-194819600	Enhancers	Fetal Thymus	thymus
13	chr3:194815200-194818600	Weak transcription	Dnd41	blood
14	chr3:194815200-194826800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:194815400-194821000	Weak transcription	Esophagus	oesophagus
16	chr3:194815400-194821600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:194815400-194827000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:194815600-194820800	Weak transcription	Hela-S3	cervix
19	chr3:194815800-194824400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:194815800-194827000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:194815800-194830200	Weak transcription	Primary T cells from cord blood	blood
22	chr3:194816000-194818200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:194816000-194823000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:194816000-194826800	Weak transcription	Fetal Stomach	stomach
25	chr3:194816000-194830000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:194816200-194818400	Enhancers	HMEC	breast
27	chr3:194816200-194819400	Weak transcription	Placenta	Placenta
28	chr3:194816200-194823000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:194816200-194823600	Enhancers	Primary B cells from peripheral blood	blood
30	chr3:194816200-194824000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:194816200-194825000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:194816400-194818400	Weak transcription	Thymus	Thymus
33	chr3:194816400-194819800	Weak transcription	Spleen	Spleen
34	chr3:194816400-194821000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:194816400-194821000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:194816400-194821600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:194816400-194823000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:194816400-194823600	Weak transcription	HSMMtube	muscle
39	chr3:194816400-194825000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:194816400-194827000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:194816600-194818200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:194816600-194826800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:194816800-194818400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:194816800-194818400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:194816800-194819400	Enhancers	NHEK	skin
46	chr3:194816800-194821400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:194816800-194824200	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr3:194817000-194818200	Weak transcription	Primary B cells from cord blood	blood
49	chr3:194817000-194818400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:194817000-194818600	Enhancers	HUES6 Cell Line	embryonic stem cell

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